Jit
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AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 2033 days agogithub.com - AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3492 days agoStructural variation caller tools using long readsCoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2969 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2347 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
By Rahul Nayak 3018 days agofaculty.cse.tamu.edu - With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from...SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
By Jit 2856 days agolbbe.univ-lyon1.fr - The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to...The Hidden Pages of Our DNA
By LEGE 32 days agoIt is enormous, billions of letters long. Some of those letters are easy to understand because they contain instructions for building proteins, the tiny machines that keep our cells alive.HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
By Abhimanyu Singh 2835 days agogithub.com - HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read...FSA: Fast Statistical Alignment
By Jit 3530 days agofsa.sourceforge.net - FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2650 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...
